4ONV | pdb_00004onv

Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate

PDB DOI: https://doi.org/10.2210/pdb4ONV/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-01-29 Released: 2015-01-14
Deposition Author(s): Manoj Kumar, P., Bhaskar, V., Manicka, S., Krishnaswamy, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.284 (Depositor), 0.297 (DCC)
R-Value Work:
0.247 (Depositor), 0.256 (DCC)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate

Manoj Kumar, P., Bhaskar, V., Manicka, S., Krishnaswamy, S.

To be published.

Macromolecule Content

Total Structure Weight: 150.89 kDa
Atom Count: 9,430
Modeled Residue Count: 1,192
Deposited Residue Count: 1,372
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 2-keto-3-deoxy-galactonate aldolase YagE	A, B, C, D	343	Escherichia coli K-12	Mutation(s): 0 Gene Names: b0268, JW0261, yagE EC: 4.1.2 (PDB Primary Data), 4.1.2.51 (UniProt), 4.1.2.28 (UniProt)
UniProt
Find proteins for P75682 (Escherichia coli (strain K12)) Explore P75682 Go to UniProtKB: P75682
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75682
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KDG Query on KDG Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain S [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain S [auth B]	AA [auth C], J [auth A], JA [auth D], S [auth B]	2-KETO-3-DEOXYGLUCONATE C₆ H₁₀ O₆ WPAMZTWLKIDIOP-WVZVXSGGSA-N		Interactions Focus chain AA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain S [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain Y [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C]	EA [auth D] F [auth A] G [auth A] GA [auth D] H [auth A] EA [auth D], F [auth A], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], O [auth B], P [auth B], Q [auth B], R [auth B], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain FA [auth D] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth C]	BA [auth D] CA [auth D] DA [auth D] E [auth A] FA [auth D] BA [auth D], CA [auth D], DA [auth D], E [auth A], FA [auth D], K [auth B], L [auth B], M [auth B], N [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain FA [auth D] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain FA [auth D] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.284 (Depositor), 0.297 (DCC)
R-Value Work: 0.247 (Depositor), 0.256 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.17	α = 90
b = 155.41	β = 90
c = 55.51	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 1.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary